An understanding of the morphogenesis and operation of hair cells requires identification of the genes expressed in these cells and of the functions of the cognate proteins. As an initial step towards this goal, we have used DNA-microarray technology to identify the transcripts present in hair cells of the adult zebrafish. After isolating pure populations of hair cells from the lagena of the inner ear, we amplified and labeled RNA and hybridized the resultant probes to oligonucleotide microarrays. To exclude genes expressed ubiquitously in epithelial cells, we conducted parallel experiments with hepatocytes and disregarded the genes that they expressed. The hair-cell transcriptome of the zebrafish includes genes involved in vesicle fusion, transcriptional regulation, and transmembrane ion movement; among these are homologs of genes that, when mutated, produce deafness in humans and mice. Additional genes encode proteins that are involved in cytoskeletal function, and might therefore contribute to the formation and maintenance of the hair bundle. These components include actin-binding and -capping proteins as well as constituents of the intraflagellar transport system. Finally, the transcriptional profile encompasses numerous genes of undetermined function. Using the molecular-biological techniques applicable to the zebrafish, we have begun to investigate the roles that some of these genes' products play in hair-bundle development.